While SDS-PAGE can reveal contaminants that are significantly different in molecular weight, it is not able to reveal post-translational modifications or other microheterogeneity in a sample. Therefore mass spectrometry analysis is needed to complement the SDS-PAGE. For small proteins, this method can determine masses within 1 Da and can thus confirm not just the identity of the protein but also how many disulfides it has (as each disulfide formation removes two hydrogens from the protein, with -2 Da mass difference). Proteins expressed in E.coli will also typically have their initiation methionine removed and in case of proteolytically processed proteins, we can confirm correct cleavage sites.
To show that we have no nucleotide contamination in the sample, we always analyse the protein by measuring its UV spectrum, typically between 340 nm and 220nm. Maximal absorption at 280 nm and a clear dip at 240 nm are typical for protein and even small amounts of nucleotide contamination will be revealed by increased absorption at 260 nm.
UV absorbance at 280 nm is also a very good way to quantify a purified protein, using calculated absorbance coefficient, and in the case of lyophilised samples, we use this to verify that we can recover the expected amount of protein from the vial after reconstitution (you can see these QC assays in use in our datasheets)
After all, if you have a vial that says 50 µg, you’d assume you’d get 50 µg out of it!